The geomagnetic-based and Global Navigation Satellite System (GNSS)-based roll angle measurement are key technologies for two-dimensional (2D) trajectory correction fuse. Influenced by the Earth’s magnetic field environment and satellite antenna patterns, the roll angle measurement accuracy may be reduced. In severe cases, significant bias may occur, resulting in a degradation of trajectory control accuracy. To address this issue, a novel Fuzzy Compensation Fault-Tolerant Control (FCFTC) strategy is proposed in these uncommon but serious situations. The FCFTC strategy which is an active fault-tolerant control strategy based on fuzzy logic rule. By analyzing the impact of roll angle bias on trajectory parameters, fault-sensitive variables are found. Subsequently, a fuzzy logic controller is constructed to achieve nonlinear mapping from fault-sensitive variables to roll angle compensation values. Moreover, variable domains and dynamic fuzzification are employed to ensure the control performance of projectiles under different uncontrolled dispersion. Monte Carlo simulation results verifies the effectiveness and fault-tolerance of the proposed strategy. This study compensates for the lack of consideration of potential roll angle bias effects in existing research. It is of great significance to improve the control accuracy, reliability, and robustness of the two-dimensional trajectory correction fuse control system.